QTL mapping of carrot resistance to leaf blight with connected populations: stability across years and consequences for breeding

Combining biparental and multiparental connected population analyses was useful for the identification of 11 QTLs in two new genetic backgrounds of carrot resistance to Alternaria dauci and for breeding recommendations. Leaf blight due to the fungus Alternaria dauci is the major carrot foliar disease worldwide. Some resistance QTLs have been previously identified in one population, but the evaluation of additional genetic backgrounds with higher level of resistance would give opportunities for breeders to combine them by pyramiding. For this purpose, two segregating populations were evaluated twice across 4 years in the same environment (1) to compare the efficiency of the single vs. the connected populations approach for characterizing the new sources of carrot resistance to Alternaria dauci; (2) to evaluate the stability of QTLs over the years; and (3) to give recommendations to breeders for marker-assisted selection. Single and connected analyses were complementary; their combination allowed the detection of 11 QTLs. Connected analyses allowed the identification of common and specific QTLs among the two populations and the most favorable allele at each QTL. Important contrasts between allelic effects were observed with four and five most favorable alleles coming from the two resistant parental lines, whereas two other favorable alleles came from the susceptible parental line. While four QTLs were consistent across years, seven were detected within a single year. The heritabilities for both populations PC2 and PC3 were high (75 and 78 %, respectively), suggesting that the resistance of carrot to A. dauci was little affected by these environmental conditions, but the instability of QTL over years may be due to changing environmental conditions. The complementarity between these parental lines in terms of interesting allelic combinations is also discussed

Carotenoid gene expression explains the difference of carotenoid accumulation in carrot root tissues

The carrot root is well divided into two different tissues separated by vascular cambium: the secondary phloem and xylem. The equilibrium between these two tissues represents an important issue for carrot quality, but the knowledge about the respective carotenoid accumulation is sparse. The aim of this work was (i) to investigate if variation in carotenoid biosynthesis gene expression could explain differences in carotenoid content in phloem and xylem tissues and (ii) to investigate if this regulation is differentially modulated in the respective tissues by water-restricted growing conditions. In this work, five carrot genotypes contrasting by their root color were studied in control and water-restricted conditions. Carotenoid content and the relative expression of 13 genes along the carotenoid biosynthesis pathway were measured in the respective tissues. Results showed that in orange genotypes and the purple one, carotenoid content was higher in phloem compared to xylem. For the red one, no differences were observed. Moreover, in control condition, variations in gene expression explained the different carotenoid accumulations in both tissues, while in water-restricted condition, no clear association between gene expression pattern and variations in carotenoid content could be detected except in orange-rooted genotypes. This work shows that the structural aspect of carrot root is more important for carotenoid accumulation in relation with gene expression levels than the consequences of expression changes upon water restriction

Breeding for carrot resistance to Alternaria dauci without compromising taste

Developing carrot varieties highly resistant to Alternaria dauci is a top priority for breeders. Meanwhile, consumers are increasingly demanding as regards final product quality, particularly taste. Bitterness is one of the five common taste sensations, but it is rejected by most carrot consumers. Therefore, providing tools for efficient plant breeding of resistant, low bitter carrots would be helpful. While resistance QTLs (rQTLs) have already been identified for carrot resistance to A. dauci, the genetic control and mapping of the metabolites involved in bitterness perception have not been addressed so far. We identified the metabolites most involved in bitterness by combining chemical and sensory analyses of a set of resistant and susceptible carrot genotypes grown in different environments. We evaluated their genetic control and heritability in a segregating F2:3 population over 2 years of field trials and searched for colocalizations between rQTLs and metabolite QTLs (mQTLs) to evaluate the link between bitterness and resistance traits. Our results suggest that it is possible to increase resistance while favoring low bitter varieties by selecting genomic regions involved in the expression of one or the other trait and counter-selecting others when r- and mQTL colocalization is unfavorable